Hi Rams, Given the ligand is identical in all structures I'd create and object from just the ligand and then write a script to align all 50 structures with that ligand object. I've done that on number of cases.
Hope it works in your case as well. Vaheh From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Subramanian, Ramaswamy Sent: Saturday, July 15, 2023 8:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Ligand superposition! Thanks Boaz, The proteins are all completely different in folds and structures! Rams subra...@purdue.edu<mailto:subra...@purdue.edu> On Jul 15, 2023, at 8:04 AM, Boaz Shaanan <bshaa...@bgu.ac.il<mailto:bshaa...@bgu.ac.il>> wrote: ---- External Email: Use caution with attachments, links, or sharing data ---- Hi, -You may want to send a query to the UCSF chimerax/chimera people. They may suggest how to this using scripts. - I have not done this on 50 structures, only on few ones. In my experience, if the proteins are sufficiently similar there is a good chance that superimposing the proteins will also bring the ligands to near superposition. -Using chimera/chimerax you can select protein residues within certain radius from the ligands, write out the pdb's and then perhaps superimpose those smaller pdb's. I have not tried this. Sorry I can't be of more help. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il<mailto:bshaa...@bgu.ac.il> Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________ From: CCP4 bulletin board on behalf of Subramanian, Ramaswamy Sent: Friday, July 14, 2023 10:49 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Ligand superposition! Hi All, I have over 50 pdb files that I have downloaded from PDB that all have the same ligand bound. I wamt to superpose the ligands (and move the protein coordinates using that matrix). The goal is for me to see how difference in ligand environments in different complexes. Is there an easy way to do it? I am sure it has been done before and I do not want to reinvent the wheel. Thanks. Rams subra...@purdue.edu<mailto:subra...@purdue.edu> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Csubram68%40purdue.edu%7Cac2bae2332d84c047c6d08db852bb97d%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638250195199675900%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2xTG40q6ub1JJMyZNnueSdZ22bpSbLOfymUPpZrmuXA%3D&reserved=0> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7Csubram68%40purdue.edu%7Cac2bae2332d84c047c6d08db852bb97d%7C4130bd397c53419cb1e58758d6d63f21%7C0%7C0%7C638250195199675900%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2xTG40q6ub1JJMyZNnueSdZ22bpSbLOfymUPpZrmuXA%3D&reserved=0> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
